The Time Long Lost
by The Ocarina of Sky
Summary: Set after Skyward Sword. What could happen when the largest Timeshift Stone ever seen is discovered? Surely nothing terrible. Right? (The author does not really know where this story is headed so read cautiously as there may be surprises)
1. Old Acquaintances

**AUTHOR'S NOTES- **I am doing this on my tablet and I am taking the 'write as you go' approach. Also, PLEASE PLEASE please tell me if you guys and galls notice any errors that I didn't after my third proofread. And lastly, before we start,** I would like to give a BIG shout out to PenguinForce for helping me with the title and other things, even if he doesn't think he did. ;)**

** Story is rated T for TEEN** because I don't know some of you handle **mild violence**, but I'll try to keep it pretty clean**. **

_**Chapter One: An Old Acquaintance and Beautiful Sounds**_

Link could not see in this non-existent light, but his keen senses told him that he was in a cave. It was cold and he heard the faintest sound of water trickling from the rough stone walls. The back of his neck prickled, the feeling of being watched. He felt a gust of warmth on his neck, heard a hiss. Link recoiled from the sensation.

_ "Boy,"_ the voice hissed. Link knew that voice. He hated it. "Boy," the voice repeated. Link turned around to confront this Demon Lord, but Ghirahim was not there.

"Dear boy, whatever could you ever do to me? You never did anything, really. You just stalled the Fates from doing their magic. But if I finish you off now..." he trailed off. Link heard him snap his fingers, and a red aura of evil light enveloped Ghirahim. He snapped again, and Link felt a weight lift from his back. "Fight me," Ghirahim continued. "Not that you'll stand a chance, though." He smirked and willed his sword to appear, causing Link to reach for his own.

Link's hand grasped the hilt of his sword, but that was all there was. His gasped in shock as he pulled an almost weightless stump of wood from the case on his back. He had more reason for astonishment when he realized that his shield, a gift from the Thunder Dragon, had been replaced by a wooden shield with a large hole in the center. "You can't kill me!" Link said as he shoved the useless items to the ground. "I know more than just how to swing a sword," he insisted, but he was really just trying to convince himself that he could stand a chance against this hated enemy.

"Oh? Well, 'swinging a sword' is, I am terribly sorry to break this to you, the only way you ever amounted to anything. But let's get on with this. I would hate ever so much for you to escape this time." Ghirahim raised his sword like a javelin, bounded forward, and struck Link directly in the shoulder. Just then, as the pain was beginning to hit, Link heard a beautiful sound. The most beautiful in all the worlds combined.

Link awoke in his bed, shuddering and in a pool of cold sweat. Zelda was there, standing over him and holding his face in her hands, singing softly. It was a song he had never heard her sing before, about facing the dusk and how there will always be a splash of white in a sea of black. Her eyes were closed and she seemed very distressed. He reached up to touch her arm.

"Zelda," he said softly, rubbing her arm with his thumb.

Her eyes flew open and her hands flew to where his were in a fraction of a second. "Link!" Her voice sounded happy that he was awake, sorry for his dream, and worried that he might not be okay all at the same time. "Are you alright? Do you want some cocoa? Should I get you a dry shirt? What about your mattress? It has to be soaked too. And what about-" Link cut her off by hoisting himself up on his elbows.

"You can go do whatever you think will make sure I'm cared for properly, Zelda," he said, fondly and not unkindly. "Honestly, it was just a nightmare. I have them all the time. I'm fine."

Zelda took her turn and interrupted _him_ this time. "But that's exactly why I should get you some cocoa and a clean shirt and- The point is, Link, you're _not_ fine and it's been more than a year already and you have those awful nightmares of yours five times a week! All because of- of me! If only I hadn't decided to-" Zelda was very flustered. She smoothed her hair back to trap some loose strands before continuing. "Link, look. I know you feel that you need to be all courageous and stuff, but you're human and I am too. A mind can't take all of this constant torment. You've only told me about one and it sounded just plain awful!"

It was true. Link had only told her about his mildest one so far, and it was nothing like the one he had had this night, or any other night, really. He shuddered.

"You don't want to know about my dreams," he whispered and touched his shoulder, the same spot where -. He didn't want to think about it.

"Link," Zelda said just as softly, overlaying his hand with hers. "I do want hear about them, when you're ready. It might make them happen less often." She squeezed his hand then rose to leave. "I'll go get that cocoa. And no buts! You need something warm to drink right now," she called from the door, trying to lighten the atmosphere.

Link laid his head back on his pillow and tried to relax, but he couldn't.

**A/N- **Yeah, I know. Super original way to start a story, right? Link has nightmares? *gasp* The next chapter might be way shorter and maybe more dull, but the other chapters will be interesting and hopefully more original with fewer author's notes and actual pieces of the plot will come together. Also, tell me how I did for a first fan-fic, any mistakes you noticed and do your regular review shenanigans blah blah blah blah. Helpful and constructive criticism is appreciated very much! :)


	2. On the Subject of Cocoa-Making

**Sorry about this shorty here (it's probably just over 950 words before author notes), but a chapter is a chapter. I put it off for way too long and only spent about two hours total on it. Anyways, I decided to take a jab at Zelda's point of view. Tell me of any mistakes that you notice because I WILL go back and edit if you see something.**

* * *

Link, Link, Link. What was Zelda going to do with Link? Just because he was the goddess's -her- chosen hero didn't mean that he had to be a tough guy all the time. She had known him since they were five and he was always the biggest teddy bear on the island. Scrape his knee when he was twelve? Cry his shorts off. Get a bad grade on his flying assessment? He'd hole himself up in his dorm room for hours or fly to a tiny sky-island far away.

She shook head, thinking about him, as she found a bottle of milk and grabbed a pottery jar from on top of the cupboard. Kikwi milk was an miraculous thing, really. It was sweet and didn't go sour for a long time. The only downside of it was deciding who had to go milk Bucha this week, as it was sometimes quite traumatic to the mind.

One day Parrow had discovered a strange new plant growing on the Great Tree that the Kikwis identified as safe. The whole village had crowded around expectantly, waiting for the fruit to be cut open. It was slimy on the inside and Kukiel had said it felt like Chu guts. But the fact that such a sweet, young girl would have her hands in Chu guts was long forgotten as everyone took a pod and popped it into their mouth. It felt like larva, but the slime was pretty good. The inside was kind of bitter, but once they added some cane sap to it, the new fruit was the best thing ever. If you ground the pods up and stirred them into some Kikwi milk, they transformed into the most wonderful drink ever. They named this new fruit and the drink cocoa as a collective.

"Do you want some help, Zelda?" There was Link again. Just because it was his duty to protect her from monsters at all times did not mean that this Kikwi milk was going to attempt to drown her.

"I am perfectly fine making you some cocoa, Link!" She heard the floor boards creak. "Don't you _DARE_ come in her, mister! I've done this a hundred times and will do it for a another ten _thousand_ times if I have to!" She took the jar's lid off and set it down on the table loudly to let him know she meant it.

"Are you sure you don't want help?" There he was, leaning in the doorway and grinning.

"Dang it, Link! I told you not to help me!" She looked him over and remembered just how sweaty his night-tunic really was. "Go change your clothes. They're saturated in your perspiration and unfit for sleeping in now," she shooed him away with her hands, but he just stayed there.

"And what if I don't want to, _Mother_?" _Mother_! She was not his mother! Was Zelda really that bossy? She decided that no, she wasn't. And she had an idea.

"If you don't," she said, raising her hand and grinning also, "I'll use magic on you!" They both knew she couldn't use magic at will unless it something big, like that one time a forty-foot tree-branch had fallen from the Great Tree and blocked off the path to the lake, but it was always a good threat.

"Oh no, whatever shall I do?" Link whined in a monotone voice. "I fear that I should simply perish of fright to the thought of your evil magic!" Zelda chuckled at the sound of Link's bad voice acting.

"Well then, if you don't want to perish, perhaps you shalt do-est as your _Mother_ says?" She snapped her fingers and told him to make like a baby dodongo if he valued his life.

He fled down the hallway obediently and shut the door behind him, making Zelda chuckle again.

She reached for the pottery jar and was pleased to see that it was generously full, tipping it over into the bottle and releasing a cascade of brown powder. Link liked his cocoa extra cocoa-ey, so she tipped it over again for good measure. She used the jar's lid as a stopper and shook the bottle vigorously. All of this cocoa making and shaking had given her good arm muscles not fit for a lady, she thought and laughed mentally.

When the cocoa was good and mixed up, she walked down the hallway to Link's room. Was that _snoring_ she heard? She knocked on the door softly, but there was no answer. Should she wake him up or let him sleep? She decided that waking him up would be better than the alternative of him having another bad dream.

"Link, I have your cocoa!" Zelda called.

"Hmm? Wassat?" Poor Link. He sounded so groggy.

"If you don't want it, I can just leave," she offered.

"Naw, just gimme a few seconds," yawned Link.

"Okay then. Tell me when you're ready," Zelda leaned against the wall and waited. Thankfully, it didn't take long for Link to open the door. As she handed him the bottle, she noticed that he had actually changed into a non-sweaty tunic.

Link accepted the cocoa jar readily and took a big drink.

"You know, there's just something about this stuff..." He trailed off.

"What about it?" Maybe he would continue if she verbally prodded and poked a bit.

"I just... The first time we found out about kwi-milk, I felt like I already knew what you were going to call it and almost exactly how it would taste... I'm not sure why, but I did," Link took another drink.

"You never told me that," Zelda frowned. How odd.

"Look, I don't feel like talking about it right now. It's late, we both need sleep, and I'm tired so I know you are too," He swirled the last little bit of cocoa around in circles before finishing it and giving the empty bottle back to her. "Thanks, Zelda," he said, patting her on the shoulder before turning back to his room and shutting the door.

"You might not remember, but Scrapper visited earlier with a message from Skipper asking you to go to Sandsea, so make sure you're ready bright and early tomorrow moring!" What would Link do without her reminding him constantly?

She heard a muffled reply of "Yes, Zelda, I know!" It probably originated from under a mountain of pillows.

"I just wanted to make sure. You_ do_ forget these things sometimes, you know," This time the only reply was silence.

Zelda stared at the bottle, then the door, then back to the bottle before retiring to her own room just a few steps away.

_Men_, she thought as she pulled her blankets up to her chest. _Can't live with them, can't live without them. _

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**Yes. Bucha produces milk out of his buttboobs. I really just said buttboobs didn't I? ._. What am I doing with my life? I just don't like the whole "Kikwi evolved into the Kokiri because their names both have K in them" theory. So in this story kikwis turned into kowkwis and the "kwis" part was lost in translation, so now we have kows. But someone thought kow looked stupid so Webster decided it should be "cows". But you'll see later in my story that none of what I just said is possible because- *is hit by a fat juicy tomato* Just think about my title.**

**You probably thought Link was going to shirtless or something when he opened the door, pervs. Nah, you aren't pervs. Just fluff seeking poodles. **


	3. Clawshotting is Monotonous

I felt bad for making you guys wait, so here's a longer chapter.

**And thank you, each and every... Eight I think?... of you guys for following my story and all of you guys who don't have accounts yet and still look at this. And for sticking with me and checking my story even though I abandoned this for I don't know how long. (Yeah, I check the stats) and also I changed the cover image. **

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Link groaned as he was shaken awake by - guess who- Zelda.

"It's too early!" He complained. "The sun is just starting to rise!" he stated, pointing to the open window.

Zelda was absolutely fuming. "I knew it! I knew you would forget! If you want to make it to the docks before tonight you had better wake up _right now_, Link!" She tore his quilt off of the bed and Link rolled up into a fetal ball.

"What did you say about the docks?" Link rubbed his eyes. "I don't remember anything about the docks."

"I _told_ you already! Skipper wanted you to come visit him and I promised him that you would. It's a long hike, so you can thank me later for the head start in the nice cool dark!" Zelda was already opening Link's chest of clothes, selecting a light brown traveling tunic, the kind with only a tiny bit of mail to cover the less bony areas of the wearer's body. "You can wear this-" she tossed the tunic to him. "And you had better take-" Link cut her off.

"Goddesses, Zelda! I know how to pack and what tunic I should wear! I'm a knight. I will take whatever I think I'll need and I'll leave whatever I don't think I might need, thank you very much," Link was very ticked off.

"Well excuse me, hero! I'm just trying to look out for you!" She pulled a day-Remlit face and pouted at him.

"Zelda. Don't do that to me!" Link pleaded. He couldn't stand the Remlit face.

"Okay, Mister. I'll stop." Zelda chuckled and set the tunic on a table next to the door. "I'll go make us some breakfast," she said as she closed the door behind her when she left.

Link sighed and rubbed his eyes. Too early. Way too early to wake up. It must have only been about five o'clock. Zelda did have a point, though, with getting up early so that it wouldn't be so hot, especially when he reached the Lanaryu desert. Too bad most of the bird statues had broken down, or he would be able to get there in under an hour. The only ones still able to work were those next to the three Dragons, but they would still cut down on Link's traveling time drastically.

He sighed and stretched. Wincing as his bare feet hit the cold wood floor, he hobbled over to the washing stand and splashed the crusts out of his eyes. Seeing the tunic on the table, he swiped it up and shoved it back into the chest. The tunic smelled of soaps and flowers and cleanliness, not at all fit for a hero like himself. He reached under his bed and pulled out a pine-green tunic, not smelling of soaps at all. It was clean, but it was a bit worn in places. Zelda had given up long ago telling him to bury it in a deep hole as he had never listened. This tunic had been through a war and back, quite literally. He would never get rid of it and would always wear it whenever and wherever he could.

He hurried as fast as he could, slipping the tunic over his head and fingers flying as they tied his boot-laces. He dunked his head into the cold water in an attempt to wake himself up a bit, barely drying his hair off at all, and was almost to the door before smelling keese eggs frying in the kitchen.

His outstretched fingers were inches from the doorknob when a breeze rustled the back of his neck. Turning around, he only saw the open window and curtain flapping from a light wind. Surely it was only the window, he thought as he slid it closed. It couldn't be... No. He wouldn't think about those things.

He opened the door without interruption and walked down the hallway, into the kitchen. Zelda was sprinkling some salt onto the cooking eggs and didn't notice him when he entered. He watched her for a few minutes before she turned around and did notice him. She made a "Bah!" sounding yelp and tossed a towel in his general direction.

"Don't scare me like that!" She complained as she flipped an egg.

Link laughed as he picked up the towel and returned it to its place on the counter. "I didn't do anything. I just stood behind you for three minutes without making a noise."

"But doing nothing _is_ something, though!"

"Whatever. I'm hungry and those look like they're done."

Zelda eyed him evilly and muttered about Link only caring about food and sleep. He pretended not to notice and let Zelda serve him his eggs, which were delicious and he made a point of telling her so. She didn't say anything during breakfast and only spoke when Link was getting ready to leave.

"Do you have your clawshots? You'll need them."

"Oh! Uh, thanks. I probably would've been halfway there before I realized I didn't have them!" Link said sheepishly. He returned to his room and kneeled at foot of his bed to open the chest that contained all of his equipment. He reached in and grabbed the two clawshots from their spot next to his bow. Fi wasn't around to minimize his gear anymore, so he would just have to carry them.

He was about to leave his room for a second time when he remembered that a sword would he nice to have too. One never knew if, more like when, a rogue band of Bokoblins would show up, hoping to make you into a human a-la-Octorock sandwich. He hesitated before grabbing the basic sword leaning against the wall, but to his relief, the sword was fully intact when he unsheathed a few inches of the blade.

He was ready now. He walked back to the kitchen, said goodbye to Zelda, and no he didn't know how long Skipper would want him to stay, and walked out he door.

* * *

What you might call a village in progress met his eyes. No one was awake yet, except him and Zelda. A few Skyloftians had yet to move to the surface so far, but they had done a great job on building a new world so far. Groose had single-handedly used his brute strength and muscle-mass to clear a large amount of trees the very first day of construction and had still insisted on building most of the houses, even those that yet to be used for a long time. He was a good worker and had mellowed out significantly since crashing to the surface with Link.

There were still some things that would have to be done in order for one to call it finished, but for now, it was perfect. There were beautiful little houses under the trees and even one _in _a tree. Everyone had pitched in to build a storage building for grain, even Stritch and Fledge. Remlits were always running to and fro just like they did in the Sky, though not ever at night as Kukiel had taken a liking towards sleepwalking outside lately. The spoiled critters had their own hut to sleep in now.

Link followed the footpath that lead to the Ancient Cistern pool, quiet as a mouse. He glanced at the Ancient Cistern as he neared the bird statue. Its entrance had once again been covered by a raging waterfall as soon as he had asked Faron if it was okay to cut down some of her forest's trees. The Water Dragon somehow always had it in her heart to look out for the little ones.

He placed his hand on the statue's beak. _To the Sky, _he thought when it glowed a dim blue. It was much weaker than usual, and the pulse he normally felt was almost non-existent. It worried him, but he only had to ponder it for a few seconds. A beam of light descended from the clouds and Link was lifted up with the same strength as always.

...***...

_Thunk_. _Sheww. ChikChikChik. Thunk. Sheww. ChikChikChik._

Clawshotting could become very monotonous to one's ears. Link thought about how nice a bridge would be, but alas, no one except him came this way yet, so he would have to deal with monotonous sounds and shoulder strain for a while. How did these things work, anyway? That didn't matter though. They worked, and as long as it works, you don't really need to understand how, was the way Link saw it. He had seen too many weird things to always demand an explanation for how something worked.

He clawshotted one last time and landed on the ground gracefully, one knee down and one hand touching the earth in a position optimized to absorb the most shock. Or, he would have if Skipper hadn't been waiting for him. He yelled from surprise and the pain of having a large metal body underneath his stomach.

He groaned and rolled off of Skipper, clutching his gut.

"Gods! I told you not to do that, Skipper! You could kill us one of these times." _To die by the hands of a robot. Fitting end for me. _"Do I have to take away your pendant?" Some time ago, he had chipped off a small shard of Time Shift stone from the large one near the desert and given it to Skipper so that the robot wouldn't have to always be within fifteen feet of his boat to operate and had personally delivered a small, but big enough, piece to his lodge as well.

"Oh my! Fo-weep! I'm sorry Link. I thought -beep- you could see me! Bo-bweep." The robot made a low, muffled sound and looked down. "You... You wouldn't really take my stone away, would you? Bwip?"

Link smiled. "You know me. I couldn't do that to you! I'm all hiss but no sting."

Skipper produced an unbelievably long string of highly pitched chirps and whistles. Obviously, he was very happy to hear that. His happy moment did not last long, however, for Skipper remembered why he had told Scrapper to tell Zelda to tell Link to come see him as soon as possible.

"Link, I need you come with me and see something, bo-bweep!" He moved his hovering hand as if to lift Link up, but he didn't have to. Link was sitting now, alert to what Skipper was telling him.

"What is it?" He asked.

"Well, bwip... You know how I've been poking around at the pirate's Stronghold? I- You had better just come see it for yourself." He was agitated and bounced around.

Link nodded. "Okay. If you can't explain it to me here, I'll go with you."

"Thank you Link! I wouldn't have bothered you if I didn't think it was important."

Link smiled again. "But I though eighty-nine percent of my visits were just because you wanted someone else to talk to?"

"But I had you come here nine days ago and you know how I don't like to bother you more than once a month, bweep."

Link considered trying to tell Skipper how it wasn't really too much trouble, again, but once a bot sets his mind on something, it's hard to get him to give up. "Let's just get in the boat, already. It'll be getting really hot soon."

"Excellent idea, fo-weep!"

...***...

"Uh, Skipper, are you sure we navigated right? This doesn't look like the stronghold."

"Buh-bip! Yes! I told you that it would be better for you to see it for yourself. Whip."

Now that there was some confirmation, Link could see _some_ similarities, but not many. The only thing in common was the size, but the stronghold would have been dwarfed by the sheer size of it. A humongous hole, maybe half as deep as the Sealed Grounds used to be and at least as wide, was layed out in front of them. A deep blue gemstone was at the bottom. A very large deep blue gemstone. But not just any gemstone.

"H-How did you do this?" Link was breathless. This must have taken ages.

"The red one found a way to preserve Big Bomb Flowers, beep. I sent Scrapper to get six-hundred and thirty of them one a long time ago, bwup."

"Why, though? What made you even think of this?" And how did Groose manage to grow that many bombs? That alone would have taken a week or more.

"Fweep, well, I had an idea about the pirates, and-"

A dagger sliced through the air and landed in the hole. Skipper unleashed the voice of a thousand sailors, swearing so much that Zelda would have chucked him in the hole like a kickball. But nothing happened for a few moments, and then another dagger followed the first. Then another. And another. There were thousands of them, every single one glowing red. Endless volleys of daggers rushed past, all of them aiming at the hole.

The last thing Link saw before he lost consciousness was a blinding flash of white, so bright that closing his eyes and burying his head in his elbows did nothing.

**The plot... It is thickening... **

**What do you think of the way I transitioned the scenes? I figured a lengthy description of flying and going from the Thunder Dragon to Sandsea would be incredibly boring for the both of us, so... Yeah. I actually "went there" and made a reference to the 1989 animated show. ._. **

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**EXCUSE FOR LATE UPDATES- Free Pokémon episodes online.** _Gotta __watch 'em all! _And I have a tendency of thinking ahead and not figuring out what needs to happen first. DX


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